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comparison SMART/galaxy/Clusterize.xml @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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children 440ceca58672
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5:ea3082881bf8 6:769e306b7933
1 <tool id="MergingDataClusterize" name="Clusterize">
2 <description>Clusterizes the reads when their genomic intervals overlap.</description>
3 <command interpreter="python">
4 ../Java/Python/clusterize.py -i $formatType.inputFileName
5 #if $formatType.FormatInputFileName == 'bed':
6 -f bed
7 #elif $formatType.FormatInputFileName == 'gff':
8 -f gff
9 #elif $formatType.FormatInputFileName == 'gff2':
10 -f gff2
11 #elif $formatType.FormatInputFileName == 'gff3':
12 -f gff3
13 #elif $formatType.FormatInputFileName == 'csv':
14 -f csv
15 #elif $formatType.FormatInputFileName == 'sam':
16 -f sam
17 #elif $formatType.FormatInputFileName == 'gtf':
18 -f gtf
19 #end if
20 -o $outputFileGff
21 $colinear
22 $normalize
23 -d $distance
24 $log $outputFileLog
25 </command>
26
27 <inputs>
28 <conditional name="formatType">
29 <param name="FormatInputFileName" type="select" label="Input File Format">
30 <option value="bed">bed</option>
31 <option value="gff">gff</option>
32 <option value="gff2">gff2</option>
33 <option value="gff3">gff3</option>
34 <option value="csv">csv</option>
35 <option value="sam">sam</option>
36 <option value="gtf">gtf</option>
37 </param>
38 <when value="bed">
39 <param name="inputFileName" format="bed" type="data" label="Input File"/>
40 </when>
41 <when value="gff">
42 <param name="inputFileName" format="gff" type="data" label="Input File"/>
43 </when>
44 <when value="gff2">
45 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
46 </when>
47 <when value="gff3">
48 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
49 </when>
50 <when value="csv">
51 <param name="inputFileName" format="csv" type="data" label="Input File"/>
52 </when>
53 <when value="sam">
54 <param name="inputFileName" format="sam" type="data" label="Input File"/>
55 </when>
56 <when value="gtf">
57 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
58 </when>
59 </conditional>
60
61 <param name="colinear" type="boolean" truevalue="-c" falsevalue="" checked="false" label="colinear option" help="This option clusterizes only the same strand reads"/>
62 <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize option for only GFF3 file format" help="This option normalize (attention!! Only for GFF3 file!!!!!)"/>
63 <param name="log" type="boolean" truevalue="-l" falsevalue="" checked="false" label="log option" help="This option create a log file"/>
64 <param name="distance" type="text" value="0" label="distance option" help="Limit the maximum distance between two reads"/>
65 </inputs>
66
67 <outputs>
68 <data name="outputFileGff" format="gff3"/>
69 <data name="outputFileLog" format="txt">
70 <filter>log</filter>
71 </data>
72 </outputs>
73 </tool>